MIT 7.016 Introductory Biology, Fall 2018 Instructor: Barbara Imperiali View the complete course: YouTube Playlist: …

Let's get going here.
So this week I'll be talking
about bacteria and viruses.
And these are really
significant topics,
because I think it's
something that we often
don't think about the
magnitude of the problems
and what kind of crises
we're approaching
with respect to the
therapeutic treatment
of infectious disease.
So what I want to try
and get home to you
this week is the variety
of different microorganisms
that threaten our
health, and just
talk to you about
the sorts of issues
that are really prominent in
the news concerning resistance
to therapeutic agents.
But in order to do that, we've
got to meet some bacteria,
meet some viruses,
and understand
that some of their
lifestyles, their mechanisms,
so that we can understand
what kinds of agents
are used and developed to try
to mitigate these diseases,
because it's only through
a molecular mechanistic
understanding of the life
cycles of viruses and bacteria
that we can understand how many
of these therapeutic agents
work and what may be happening
in resistance development.
Now I find this particular
slide a little daunting,
but I want to point out to you
that it concerns the world's
deadliest animals.
So we worry a lot about
tigers, and sharks,
and things like that,
nasty poisonous snakes,
bites from dogs with
rabies, and so on.
I'm going to leave this black
bar here, sort of unmentioned.
I don't know what year this is,
but if we talk about daunting,
that's pretty serious.
And then the biggest killer on
this screen is the mosquito.
But it isn't actually
the mosquito,
it's the protozoal
that the mosquito carries
from one person to another
that really make that such
a serious consideration.
But what's not here are all
the bacteria and viruses that
actually are far more serious.
And the numbers
on the next stage
will show you just quite how
shocking these numbers are.
If you're interested
in infectious disease
as a field, because I think
anyone going towards MD,
MD/PhD infectious
diseases, it really
is a critical area that we
have to get to grips with.
There are not enough
vaccines in the world.
There is not enough
treatment with a very microbe
specific anti-infective agents.
So I encourage you
to look at the CDC.
There's a few other
places where there's
loads of information collated,
such as the NIAID, which
is the NIH Center for
Infectious Disease,
and the World
Health Organization.
So there's lots of places
where you can find stuff out.
So what we're going to be
talking about in the next three
classes are our smallest
enemies, things like bacteria,
fungal infections from things
like yeast or Aspergillus,
which would cause candida
and aspergillosis.
Protozoal disease
we won't mention,
but those are the
types of diseases
that are carried by things
like ticks, mosquitoes,
tsetse flies.
We think of those as
the infectious agent,
but it's really what those
organisms carry and cause
the spread of disease
that's important there.
And we won't either talk
about prion diseases, which
are the diseases
that don't involve
an infectious
microorganism, but are
believed to be spread
from protein to protein
through the nucleation of new
prions from existing prions.
What we'll focus on
in the first class
is bacteria and in the
other two on viruses,
with an eye to
looking at antibiotics
and antiviral agents, how they
work, where they go wrong.
And this is where the
numbers get fairly shocking.
So for example,
bacterial infections
of the lower respiratory tract,
that's deep in the lungs,
cause 4 million deaths a year.
Think back to the numbers you
just saw on that first slide.
These are things like
strep pneumoniae,
Klebsiella pneumoniae.
They're called pneumonias
because they're
infectious diseases of the
lung, but the organisms
that cause them are of the
Streptomyces, and Klebsiella,
and Staphylococcus
aureus specifically.
But there are others that
cause lung infections and lower
respiratory disease.
These are particularly
troublesome in areas
where the atmosphere is bad.
In big cities where there's a
lot of insult from emissions
and such that make
the lungs weaker,
then these sorts of
organisms can really
take a hold more readily,
so they are more serious.
There are many,
many microorganisms
that cause pneumonias.
And sometimes it's
a real problem
to track down the precise
microorganism, which
makes the issue of treatment
really difficult, really
So I'm going to talk in a minute
about absolute identification
of infectious agents, so we can
do better jobs of specifically
targeting the causative agents.
Diarrheal disease–
2 million deaths.
These are organisms like
Campylobacter jejuni
and Salmonella enterica.
We tend to have these
crises, because romaine my
is contaminated with infection.
There are very few deaths
in the developed world.
We get down to
that very quickly,
say stop eating Romaine
lettuce until we figure out
what's going on here–
very, very few.
But once again, in
the developing world,
these can run rampant.
And they can grab small
children and older people who
are already compromised,
already a little bit not quite
with strong immune systems,
and people generally
die of dehydration, because
these diseases really
hit the GI tract.
It causes leaking us in the
GI tract and really, really
serious diarrheal disease.
So those are the bad boys there.
But once again, there
are many others.
Tuberculosis is yet
another really serious
infectious disease caused by
Mycobacterium tuberculosis,
that's the main one of the
mycobacteria that is a threat.
It used to be called
consumption in the old days,
because people almost looked
consumed by the disease.
They would just get
thinner and thinner.
Literally it was
a wasting disease.
People would be sent up into
the mountains of Switzerland
to try to recover
from consumption,
to where the air is
clearer and cleaner,
and maybe hope that
they can recuperate.
But TB– look at these numbers.
In 2015 there were almost
10 million new cases.
There are about 1.2
million deaths from TB.
A serious situation with
TB is that it's often
found co-infecting with the
HIV virus, where you just
can't fight the TB.
So eventually, if you're
infected with the HIV virus,
it's the TB that gets you
due to the weakening caused
by the infection with TB.
So these numbers are
shocking in light
of the numbers I showed you
on the previous slide, right.
Look at these numbers if you go
to snakes and things like that.
They're meaningless
numbers compared
to infectious diseases.
So now, and I'm going to talk to
you about the origins of this,
many, many infectious
agents that we thought we
had conquered–
we thought we could
take care of it.
You just take this course of
antibiotics and you're off,
you're set.
But now, because of the
rapid mutation rates
in bacteria and viruses,
certain pathogens
have completely
worked out mechanisms
to escape therapeutic agent.
And I'm going to talk to
you about those mechanisms
towards the end of this class.
So basically you can
dose a person one day
with a normal dose of
an antibiotic agent,
and then 10 months later
that normal dose or 10 times
or 100 times that
dose stops working.
Why is that?
It's due to resistance
acquisition due to rapid cell
division and mistakes made on
replication and transcription,
that then may one
in a million times
confer an advantage
on the microorganism.
All of a sudden the
drugs don't work anymore.
The WHO and various
community notice boards
call this set of infectious
agents the escape pathogens.
It helps us remember
which ones these are,
because these are pathogens
that escape treatment,
because they've
developed resistance
to multiple drug cocktails.
So commonly, when someone
has a particular disease
they don't take one drug,
they take two or three
to hit lots of pathways
at once in the hope
that resistance
won't develop fast.
But the escape pathogens
have collectively
acquired resistance to
several antibiotics,
meaning there's
no good treatment.
So the letters of escape stand
for Enterococcus faecium,
Staph aureus, Klebsiella
pneumoniae, Acinetobacter
baumannii, Pseudomonas
aeruginosa, and some
of the Enterobacter species.
Some of these infectious
agents are what result from–
I always say this wrong–
nosocomial infections.
Does anyone know what those are?
These are infections that
people get in hospitals.
So Tom Brady had
a knee operation.
He got an infection in his knee
that came from the surgery,
These are hospital
acquired infections,
because you can't sometimes
clear an area enough,
and there's infectious
agents around.
So Acinetobacter baumannii
was dubbed the Iraqi Bug
for many, many years, because
the vets coming back from Iraq
were going to
military hospitals,
and these were
abundant with cases
of Acinetobacter baumannii.
So that moved on to the
escape pathogen list.
So these are things
to watch out for.
It's the reason that
nosocomial infections–
I hope I'm saying
it right, otherwise
you're going to go off
and Google it and realize
I said it wrong.
It's the reason why old school
physicians wore bow ties
and not ties.
Can you imagine why?
So if you're wearing
a tie, which I seldom
wear to be honest, and you're
working over a patient,
the tie can be the thing
that carries the infection,
because it gets closer
to infected areas.
This is old school stuff.
And so originally the
physicians wore bow ties
in order to distinguish
themselves as important people,
but not to wear ties that
might carry infectious agents.
That's sort of a scary thing.
So with all this
said, let me just
lead you in to talk about
bacteria antibiotics
and resistance development.
So we often name bacteria
somewhat by their shape.
So the long rod
shaped ones are cocci.
The round ones are cocci.
The rod ones, whatever they
are, come on one of you.
And then what did
the rod shape ones?
I had a blank moment.
So the rod shaped
ones are bacilli.
And then there's
some others that
have a different morphology
like Campylobacter jejuni
that have kind of
a corkscrew shape.
And that's thought to be
important in their motility,
digging through
the mucous layers
in the epithelial layers.
So here I show you several
shapes of bacteria.
And I'm just going
to, once again,
reinforce what diseases
some are associated
with and some other diseases
that you might be surprised by.
So yes, we know about
salmonella and the E.
coli and food poisoning.
But Helicobacter
pylori, which is
one of these
flagellated bacteria,
can infect the stomach.
It's often the cause of ulcers.
So it's a causative
agent of stomach ulcers,
but that has in turn led
to a considerable risk
factor in stomach cancer.
So what we thought
was just an infection
causes a constellation of other
problems, including cancers.
And more and more
microbial agents
are now associated with cancers,
in particular the viruses.
Neisseria, these come
along with the sexually
transmitted diseases
such as gonorrhea.
Neisseria meningitidis is the
one that causes meningitis.
It is a very, very often fatal
infection of the meninges.
Staph aureus lots of
infections around the body,
just gruesome things
like cellulitis,
wound infections, toxic shock.
bacteria, I've already
mentioned– the pneumonias,
and then Campylobacter.
And now another complicated
factor of infection–
so I talked to you about stomach
ulcers and stomach cancer.
Another thing that seems to be
coming along with infections
is autoimmunity.
So in the last section of the
class you heard about immunity
and you also heard
about tolerance,
that we don't react to
things that are ourselves,
otherwise we'd be
in deep trouble.
Autoimmunity can
suddenly pop up from
certain bacterial
infections, because bacteria
tend to cloak themselves
with unusual sugar
polymers and other
kinds of structures
that the body doesn't
really know what to do with.
And in some cases
they kind of mimic
things that are
in the human body.
So they they are mimetics
of normal structures
in the human body.
And the body just doesn't
notice them at all.
And then there are
incidences where
certain bacterial
infections later on
cause autoimmune disease.
So a bacteria may come along.
It may have something that looks
kind of like something human,
but not quite.
The human body responds,
develops antibodies,
and then they cross talk back
to aspects of our physiology.
So Campylobacter jejuni is
often a contaminant in poultry.
It's a severe GI infection.
But later on people get
diseases such as Guillain-Barre,
which is a neuropathy where
the ends of your limbs
become numb and non-functional.
So there was a famous
football player,
the one they called
"The Refrigerator," who
had a serious case of
Guillain-Barre resulting
from very much an
infectious disease, which
converted into autoimmunity.
So let's now look at
antibiotic targets.
And to look at
antibiotic targets,
I think the first
clear place to look
is at the bacterial cell wall.

Now when we first started
talking about prokaryotes,
things that include bacteria,
we talked about the fact
that these single
celled organisms
have to have a robust cell
wall to prevent osmotic shock.
They have to have
some kind of thing
to keep them from
taking up too much water
and basically exploding
because of osmosis.
Water floods in to balance
the salt concentrations.
So they have a
complex cell wall,
which is made of a macro
molecule called peptidoglycan
And it's usually one word,
but I want to just underline
peptidoglycan because it's
a fascinating polymer that's
made up of peptides and
linear carbohydrate polymers.

So if you look at this
typical bacterium,
this is just a cartoon
of the peptidoglycan.
So it's a cross-linked
polymer, we
in one direction it has
repeating carbohydrate units.
I'm not drawing those complex
hexose structures there.
I'm just drawing
it in cartoon form.
And those are carbohydrates
known as NAG and NAN.

NAG is N-Acetyl Glucosamine.
It's a hexose sugar.
NAN is N-AcetylMuramic acid.
It's another modified sugar.
And on the one of
those sugars, there
is a reactive site that allows
you to basically cross-link
these polymers into a mesh work.
So it's a feat of engineering
to build this amazing polymer.
It starts being built on the
inside, on the cytoplasm.
And then the components get
flipped onto the other side
of the cytoplasm of bacteria.
Then they get
polymerized in place
to make this complex
mesh work of a polymer
that creates the rigidity
of the bacterial cell wall.
It's generically known
as a peptidoglycan.
Different bacteria have
different peptidoglycans.
There are several
modifications that
might be specific to
particular bacterial sera
But this is the
generic structure,
where you have a polymer
that's built of sugars.
You can recognize the
sugar structure there
going in one direction and
the peptide component that
cross-links across in
order to make this mesh.
And bacterial wall have
different amounts of this,
but it'll build up to a
really strong, rigid mesh
work that's permeable to things,
small molecules and water.
There is holes, and so on.
But it creates a
mechanical rigidity
so that osmotic shock doesn't
occur on the bacteria.
Any questions about that?
Does that makes sense?
So that, in a sense,
it's their exoskeleton,
if you want to think
about it like that.
So the properties are rigid.
Without it, the bacteria
would suffer osmotic shock.
And it's plenty permeable
to allow 2-nanometer type
pores in order for nutrients and
water to go into the structure.
– –have E. coli growing here.
And it's living.
You can see it start to grow.
Here we add penicillin.
We're going to see
these bacteria–
PROFESSOR: These are
bacteria, rod-shaped bacteria.
– There wasn't any
microphone on this, so–
PROFESSOR: And I'm going to
ask you to just keep watching
this kind of carefully.
– There goes another
one, boop, boop.
– Poking holes in the cell
wall, boom, bacteria is dead.
PROFESSOR: Look at some of
the bacteria disappearing.
All right, I guess
OK, then we're going to–
So we're going to leave it.
Let's go back one.
OK, now what was that?
OK, so I've told you bacteria
would suffer osmotic shock
without peptidoglycan.
Those are bacteria
that you see popping,
as the person who
was talking said,
because the peptidoglycan
cannot be made.
There is an antibiotic
that's added.
It is penicillin that's
added to the bacteria.
And it stops– as bacteria grow,
they have to make a bunch more
peptidoglycan, because
if you're doubling,
you've got to make
twice as much peptido–
you've got to double the
amount of peptidoglycan.
If you have something
that inhibits
the peptidoglycan
being made, you
have a bacterium that's trying
to stretch out what it has,
it's not resistant
to osmotic shock.
And what you saw was the
bacteria basically undergoing
cell death via osmotic shock,
pretty graphic, pretty visual.
So penicillin was one
of the first antibiotics
that was described
for the treatment
of bacterial infections.
And we'll go to the timeline
of that in a moment.
So when we talk about bacteria,
the original definition
of bacteria is in three
different subtypes,
gram-negative, gram-positive,
and mycobacterial.

This is actually the
first way that people
would take a look at your
cell– at the bacterial cells
and diagnose roughly what
kind of bacteria they were.
Did they fall– which
of these broad families
did they fall into?
Because it would
help in defining how
you would treat the
infectious disease.
So I want to show you the
difference between the cell
wall of these various
types of bacteria.
And the truth is, if you
have an infectious disease,
your wish is, if you had
to pick one of the three,
that you have a
gram-positive disease.
And I'll explain why
that is in a moment,
because it's all to do with how
drugs can get into the bacteria
to inhibit vital functions
in order that they die
and they don't take
over your system.
So let's look first at
gram-positive bacteria.
They're shown here.
This is a section
of a bacterium.
Gram-positive have
a single cell wall.

And they also have a thick
layer of peptidoglycan.

So they gain
rigidity by basically
having an extracellular
thick layer of peptidoglycan
coating them.
There is a schematic of it here.
So here would be
the inner cell wall.
And here would be
the peptidoglycan,
shown in orange and pale,
buff-colored circles.
So that would be where
their peptidoglycan is.
And then there are some
other glyco conjugates that
actually stick out beyond that.
But there is only one
cytoplasmic membrane.
That's the standard
double bilayer.
And the peptidoglycan is
quite thick, relatively,
20 to 80 nanometers across.
So that's how wide it is.
And you can, if you've
got a– if you've
stain a bacterium
under a microscope,
you would see that, the
thickness of that wall,
but the absence
of a double wall.
The gram-negative bacteria
have a double wall.

The inner membrane
is pretty standard.
It's just typical phospholipids.
It looks like the inner
cytoplasmic membrane
of the gram-positive bacteria.
And then it has an outer wall.
So the inner
membrane is typical.
And then the outer
wall has one leaflet
that looks kind of normal.
And then it has a second leaflet
that's sort of decorated,
honestly, like a Christmas tree.
There is all kinds of
things sticking out
there that interact with hosts
that they infect, and so on.
And the space
between the two walls
is called the periplasmic
space, because it's between.
It's not the cytoplasm.
It's what's called
the periplasm.
Now, what's interesting
about these,
the gram-negative bacteria,
is they have quite a bit
less peptidoglycan, only
about 7 to 8 nanometers.

So that's pretty interesting.
But they sort of gain robustness
from that second wall structure
that's coating on the outside.
Now, their challenge with
gram-negative bacteria relative
to gram-positive bacteria is any
drugs you develop have to make
a pretty–
if they're targeted at
intracellular sites,
they have to get through two
walls, not just one wall.
So they are harder to treat.
And they also have a
lot of characteristics
that make them more prone
to resistance development.
So I want to point out to you,
on this electron micrograph,
you can actually see the double
wall, the dark band of space
and then another dark
band, whereas here you
see a thin single
wall, but you see
a lot of junk on the outside.
Is everyone seeing
the differences just
to look at them?
OK, so what's this
gram thing about?
What does this stand for?

It simply stands for a chemical
dye that stains peptidoglycan.
And it was invented or
discovered by Professor Gram.
That was his name.
So when someone says you got
a gram-positive infection,
infection, it's how
those cells look when they've
been treated with this stain.
Gram positives show up
very positive to the stain
because there is a
lot of peptidoglycan
on the outside that absorbs the
dye and shows a strong color.
The gram-negatives don't show
very well with a Gram stain,
because the peptidoglycan
is tucked in the periplasm,
not on the outside of the cell.
So if someone does a quick
check on a bacterial streak
or an infection
that you have, they
might treat it
with the Gram stain
and say gram-positive
or gram-negative just
based on that simple
color analysis.
And so in one case,
the peptidoglycan
is abundant and accessible.
In the other case, it's very,
very much thinner and less
accessible to the dyes.
Now, this probably looks
like stone-age stuff
to you, because how
much can you learn
by these simple
colorimetric stains?
We're certainly moving in very,
very different directions.
But let me just finish off with
the third type of bacteria,
the mycobacteria, which include
Mycobacterium tuberculosis.
And they have a different
kind of wall, again.
And they're pretty unusual.
And they are really,
really hard to treat,
because it's almost impossible
to get therapeutic agents
into mycobacteria.
I used to work on a team
with Novartis in Singapore.
And they said, doing
anything with mycobacteria
was like trying to do
biochemistry on a wax candle,
You just can't work
with it, because they
have a thick additional wall
that's kind of different again.
Did you have a question?
Sorry, I thought I
saw your hand up.
So what they have
is a typical cell
wall then some
peptidoglycan, but then they
have this thick
mycobacterial layer
which comprises what are
known as mycolic acids, which
basically add this thick layer
of greasy hydrophobic material
on the outside of the
mycobacteria that's
pretty impenetrable.
The cell wall is
quite different.
It doesn't have an outer coat.
It's like gram-positives
in that respect.
But it doesn't
stain very strongly.

So it has a weak, what's
known as Gram stain.
So sometimes if
you've got something
that gives a sort a so-so
response to the Gram stain,
you might say, oh, it
looks like a mycobacterium
because of what's happening.
Now, mycobacteria
TB is a huge threat,
because its treatment, its
current treatment– and it's
the same treatment that's
been around for, like, 30
years or something– is
a treatment with four
different antibacterial
agents that
hit a bunch of different
sites in the lifecycle
of the bacteria.
It includes these
compounds shown here
which are isoniazid, rifampicin,
ethambutol, and pyrazinamide.
And it's a six-month treatment
with those medications,
so handful, four different
medications for six months.
So what they were realizing
in the developing world
is that there was
terrible compliance.
The drugs are cheap, but
there was no compliance.
People just were not taking the
pills, because they're like,
I'm tired of taking these
pills every day for six months.
So what was developed was what's
known as the DOTs program.
Has anyone never heard of this?
Is anyone interested
in infectious disease?
It was a situation where it
was a social system set up
in order to make
sure people took
these drugs every day for six
months in order to comply.
So social workers would go to
the villages in remote areas
and watch people
take the medications.
So it's directly
observed treatment
to make sure they followed
through, because if they had
regular TB, not very resistant
TB, you could overcome it,
provided that you took
these medications.
But still, it's a hugely
debilitating thing
to have to deal with
these treatments.
Now, there are
two strains of TB.
One is called MDR-TB.
And the other ones called
XMDR-TB You'll occasionally
hear of these on TV programs.
MDR is resistant to three
of the four medications.
And XMDR, which stands for
extremely MultiDrug Resistant,
is resistant to every single
one of those medications.
New medications, different
mechanisms of action
are sorely needed.
All right, this is
just what things
look like with the Gram stains.
So here you see gram-positive
Bacillus anthracis.
That's the deep purple rods.
You know that's a
gram-positive because it's
a deep purple stain.
The other cells in this
picture are white cells.
So you can really pick
out the gram-positive.
This is the structure
of the chemical dye
that stains peptidoglycan
through absorbing
into the peptidoglycan.
It's a very sort of
physical interaction
of the dye with the polymer.
And over on this slide, it's
a mixture of gram-positive
and gram-negative.
And you can pick up
the gram-positive
and differentiate them from
the gram-negative, which
just stains sort of
kind of weakly pink.
And then mycobacteria, which
are formerly gram-positive,
don't stain very well
because of that thick mycolic
acid hydrophobic wall.
So what would you do nowadays?
Would you pull out a stain
and drop it on bacteria
and get some vague response?
What's open to you now
in the 21st century?
You have a tiny
sample of a bacterium.
Grow it up.
What would you do?
You could tell
exactly what it is.
PROFESSOR: Yeah, you'd
PCR up the genomic DNA
and then go match it, because
the thing that we, in addition
to the human genome,
there are thousands
of pathogenic bacteria sequences
that are completely annotated,
The [INAUDIBLE] has a massive
compilation of these sequences.
And you just go and you
find out what the bacterium
is based on the sequence.
So now rapid
sequencing efforts–
maybe they're just a few number
of key places in a genome
that you would go towards and
just do a really fast array
and figure out what's there and
within what bacterium it is,
which gives you a much better
clue as to how to treat it
than the vague,
ambiguous stains.
So even though stains keep
going, there is now other ways.
Unfortunately, not everyone
has the instrumentation
to do rapid sequencing.
So nowadays, there
is a lot, lot,
lot of interest in faster
dipstick sorts of tests
that can distinguish between
different bacterial strains
by, for example, interrogating
that coat of glyco-conjugates
that's on the outside
of the bacteria,
dipstick paper tests
that can give you
an idea of what
organism and what
serotype so you can move forward
and do a much more rational
treatment of those organisms.
OK, let's see what's– yes.
All right, so where did the
antibiotics first come from?
Any questions so far?
OK, so where did the first
antibiotics come from?
From a couple of
accidental discoveries.
Who has heard of the
Fleming experiment?
Who knows about that
discovery of penicillin?
Yeah, so there was an
original observation
that predated that which
sort of suggests that Pasteur
was a pretty smart guy,
because he contributed
in a lot of different areas.
He discovered that some bacteria
tend to release substances
that kill other bacteria.
That was in the 1870s.
Then later on, there
was another sort
of spread of antibiotic agents.
And it came with the
discovery that we had things
like arsenic
derivatives actually
showed some value in
treating the organism that
causes syphilis.
So talk about the
treatment being–
the cure being worse
than the infection.
People were being
treated, seriously,
with these arsenic derivatives
in the hope of wiping out
the infectious agent
that caused syphilis.
But you know, sometimes
it was a mixed bag.
But where things started to get
a lot more interesting was that
in 1928, there was this sort
of famous historic story
of Fleming discovering
that some bacteria seemed
to be inhibited by a particular
agent that came from a fungus.
And this was the
origin of penicillin.
So he would have a Petri dish
where he was growing bacteria.
And he noticed that in
some of his samples,
there was inhibition
of bacterial growth
due to an exogenous
agent that had somehow
contaminated the plates.
So in that story,
that was the substance
that was named as penicillin.
The mold from the–
mold is the fungus–
actually inhibited the growth
of staphylococcus bacteria.
And it was called penicillin.
And then a lot
more time went by.
But in the 1940s, the active
ingredient was discovered.
So 1940s is sort of slap
bang about, I would say,
a couple of years into
the Second World War.
And they were able to mobilize
the production of this agent.
Towards the later
end of the war,
people had penicillin
available to them.
And it's basically
pretty well believed
that, if it wasn't for
the antibiotic agents that
you know, the war ended in 1945.
If it wasn't for those
agents that emerged,
there would have been way way,
way more deaths from the war.
As it was, there
were way too many.
So penicillin was
the first antibiotic
that was discovered with a
discreet mechanism of action.
And it was discovered at a
very, very important time.
So that was all great news.
Penicillin was produced widely.
Some of you may be
allergic to penicillin.
There are other
options nowadays.
But it's the cheapest
and most viable
of the first-line antibiotics.
Here we go.

And this thing, this pointer
has a mind of its own.
It sort of changed its mind.
But the problem was
the bacterial species
started to survive treatment due
to development of resistance.
And all of a sudden, something
that worked really well
wasn't working anymore.
So let's try and think
about peptidoglycan,
what penicillin looks
like and what it does,
and how penicillin
resistance emerges.
Those are the three things
I'm going to cover here.
OK, so what does penicillin do?
Penicillin stops the formation
of this big macromolecular
peptidoglycan polymer by
stopping the last cross-link,
stopping the
chemistry that happens
to join the peptide chains to
make a cross-linked polymer.
And anyone who is in the
mechanical engineering area
will know that polymers
that are just strands
are much weaker
than polymers that
are crossed-linked
structures which
have tensile strength
in both directions.
So the uncross-linked
peptidoglycan was weak.
And what penicillin
specifically did
was inhibit forming
that cross-link.
What does penicillin look like?
Here it is.
It's a cool structure.
It's what's known as a natural
product, five ring, four ring,
an interesting structure.
And what it would do is it
would interact with the enzyme
the cross-linked
the peptidoglycan
and basically stop it
dead in its tracks.
What did the bacteria do?
The key part of this structure
is this four-membered ring
within amide bond in it.
The bacteria evolved an enzyme
to chop it open basically
making it completely inactive.
So beta lactamase was evolved
in the bacterial populations.
It was probably derived
from some other enzyme that
did some useful
function, but not
targeted to the penicillins.
But the bacteria
started to survive
because they made a ton of an
enzyme called beta lactamase.
And then it completely
stopped working.
So the chemists came
up with other options,
because they said, well, you
know, if that doesn't work,
we've got other
antibiotics in our arsenal.
And there is a
compound that was used
for years as a last line
of resort antibiotic known
as vancomycin.
It was very, very important,
so very serious infections,
and really preserved
for that use.
And they thought that
vancomycin might be a drug that
just couldn't be defeated.
This big molecule
here is vancomycin.
This little piece of peptide
is actually the peptide
that's in that cross-link.
And vancomycin
basically, like a glove,
sat on that piece of peptide and
stopped it being cross-linked.
And what did the bacteria do?
They evolved a set of
enzymes to completely change
that little piece of
peptide into something
that bound more poorly,
giving you resistance
to vancomycin as well.
So when there is
one drug involved,
it's pretty easy to get
resistance quite quickly.
You just mutate one enzyme and
you get a resistant strain.
And the enzyme that can beat
the antibiotic will win.

If you've got a compound that
takes five different enzymes
or an antibiotic that has a very
complex mechanism of action,
you might say, well, this is
never going to be defeated.
It took five additional
enzymes to evolve
to make the peptidoglycan
a different structure.
And it's not that
within every bacterium,
you mutate five
different enzymes
and get them all
working as a team.
What was happening
in these infections
is that a plasmid with
the set of enzymes
was being passed around
amongst bacteria.
So a new bacterium could acquire
resistance to this compound
without evolving a whole
bunch of new enzymes,
but rather by lateral
transfer of plasmids
encoding the genes that it
took to make the vancomycin
All right, so let me just
tell you a few of the targets.
And then there is one
movie I want to show you
that's kind of cool.
So currently, when we inhibit
bacteria with antibiotics,
there are a number of
essential processes
that are targeted with
common antibiotics.
So this would be a
typical bacterium.
One target of action is DNA
synthesis and DNA polymerase.
And the enzyme
that is targeted is
one we've talked
about, topoisomerase.
And that is inhibited
by the fluoroquinolones
such as ciprofloxacin that
actually targets specifically
the bacterial polymerase.
So that's one way,
inhibit DNA replication,
bacteria can't divide.
Another set of
antibiotics are those
that inhibit protein synthesis.
So in particular,
you know the tunnel
that comes out of the ribosome
where the growing polypeptide
chain emerges after
reading the messenger RNA
and translating the
messenger into protein?
There are antibiotics to
basically stick in that tunnel
and stop protein synthesis.
And those are things
like the aminoglycosides.
And they block exit
from the ribosome.
But you could imagine
that mutating.
There are the ones that
inhibit cell wall biosynthesis
that I've already talked
to about, the penicillins,
the vancoymcin.
And then there are others
that inhibit folate synthesis.
And then there is a
lot of synthetic drugs,
but also a lot of
natural product drugs.
So both nature and
chemistry have teamed up
to inhibit all of
these essential steps.
OK, so how do you test
for antibiotic resistance?
You use plates where you're
growing particular strains
of bacteria on a plate.
This would be a colony.
And it's growing outwards.
Where there is a colony but
there is no growth around it,
it means there is something
in that plate that
is inhibiting bacterial growth.
So these are very
clear types of ways
that people check
to see if bacteria
have become resistant to drugs.
You would look for that
zone of inhibition.
Does it disappear with some
of the resistant strains,
for example?
And these get
pretty sophisticated
now where you can test a
bunch of antibiotics in one
go, where each of
these colored dots
represents an area
where there is treatment
with one antibiotic or another.
So what's the problem?
The problem is this
graph, that as soon
as an antibiotic is introduced,
just a few years go by.
And there is resistance
to that antibiotic.
So resistance basically
is the gradual acquisition
of machinery to
somehow inactivate
the antibiotic treatment.
So if you take a
look, here on the top
is where the drug is introduced.
And on the bottom is when
resistance was developed.
So let's go to something
we're familiar.
Here is penicillin, people
introduced about 1940
to the general population.
By about '47, there was
resistance to penicillin.
And you can see, this is really
just a really serious sort
of series of events.
So what I want to show you
was resistance in action.
And that'll be the last
thing I talk about today,
because I just want to
give you a feel for what
does resistance look like.

So this was an
experiment that was
done at Harvard on just a
visualization of resistance
I think what's so
fascinating is you could then
go back to the plate and
pluck the first pioneers who
crossed that line and
find out what that was.
What was that mutation that
let the population expand,
and so on?
So you could really map out the
entire evolution of very, very
strong resistance.
So in the next class,
I'll talk to you
about resistance mechanisms.
And then we'll talk about
viruses and resistance
to antivirals.

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